20180725-2-Gastroc-002-powder_S2 vs 20180725-3-Gastroc-002-powder_S3

ATAC-seq on motrpac

Report generated at 2018-10-27 03:55:57

Pipeline type: ATAC-Seq

Peak caller: MACS2

Flagstat QC (raw BAM)

rep1rep2
Total4333941265787412
Total(QC-failed)00
Dupes00
Dupes(QC-failed)00
Mapped4306294364369053
Mapped(QC-failed)00
% Mapped99.360097.8400
Paired2458407832781498
Paired(QC-failed)00
Read11229203916390749
Read1(QC-failed)00
Read21229203916390749
Read2(QC-failed)00
Properly Paired2406613031075436
Properly Paired(QC-failed)00
% Properly Paired97.890094.8000
With itself2426091831308026
With itself(QC-failed)00
Singletons4669155113
Singletons(QC-failed)00
% Singleton0.19000.1700
Diff. Chroms5233359446
Diff. Chroms (QC-failed)00

Flagstat QC (filtered BAM)

rep1rep2
Total1697283018904942
Total(QC-failed)00
Dupes00
Dupes(QC-failed)00
Mapped1697283018904942
Mapped(QC-failed)00
% Mapped100.0000100.0000
Paired1697283018904942
Paired(QC-failed)00
Read184864159452471
Read1(QC-failed)00
Read284864159452471
Read2(QC-failed)00
Properly Paired1697283018904942
Properly Paired(QC-failed)00
% Properly Paired100.0000100.0000
With itself1697283018904942
With itself(QC-failed)00
Singletons00
Singletons(QC-failed)00
% Singleton0.00000.0000
Diff. Chroms00
Diff. Chroms (QC-failed)00

MarkDuplicate QC

rep1rep2
Unpaired Reads00
Paired Reads939580710681883
Unmapped Reads00
Unpaired Dupes00
Paired Dupes9093921229412
Paired Opt. Dupes45674432
% Dupes/1000.09680.1151

Library complexity QC

rep1rep2
Total Read Pairs917137110562098
Distinct Read Pairs83236669372160
One Read Pair75446898295254
Two Read Pairs715743974306
NRF = Distinct/Total0.90760.8873
PBC1 = OnePair/Distinct0.90640.8851
PBC2 = OnePair/TwoPair10.54118.5140

NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally


Enrichment (strand cross-correlation measures) QC

rep1rep2
Reads83110199357705
Est. Fragment Len.00
Corr. Est. Fragment Len.0.19490.1503
Phantom Peak7060
Corr. Phantom Peak0.15810.1295
Argmin. Corr.15001500
Min. Corr.0.11280.1218
NSC1.72721.2340
RSC1.81353.7017

NOTE1: For SE datasets, reads from replicates are randomly subsampled.
NOTE2: For PE datasets, the first end of each read-pair is selected and the reads are then randomly subsampled.


rep1
rep1
rep2
rep2

Enrichment QC (Fraction of reads in MACS2 raw peaks)

rep1rep2rep1-pr1rep2-pr1rep1-pr2rep2-pr2pooledppr1ppr2
Fraction of Reads in Peak0.26700.14320.29310.17530.29220.17420.18960.20340.2025


Reproducibility QC and Peak Detection Statistics

overlapIDR
Nt8720426262
N19309241952
N23876014980
Np10777547189
N optimal10777547189
N conservative8720426262
Optimal Setpprppr
Conservative Setrep1-rep2rep1-rep2
Rescue Ratio1.23591.7969
Self Consistency Ratio2.40182.8005
reproducibilityborderlineborderline

Overlapping peaks


IDR (Irreproducible Discovery Rate) peaks


Enrichment QC (Fraction of reads in overlapping peaks)

rep1-rep2rep1-prrep2-prppr
Fraction of Reads in Peak0.11470.18900.04450.1302


Enrichment QC (Fraction of reads in IDR peaks)

rep1-rep2rep1-prrep2-prppr
Fraction of Reads in Peak0.06050.12770.02600.0855


IDR (Irreproducible Discovery Rate) plots

rep1-rep2
rep1-rep2
rep1-pr
rep1-pr
rep2-pr
rep2-pr
ppr
ppr